Toxicogenomic profiling of chemically exposed humans in risk assessment

Mutation Research - Reviews in Mutation Research

Volumn 705, Issue 3, 2010, Pages 172-183

  McHale, Cliona M ^a   Zhang, Luoping ^a   Hubbard, Alan E ^a   Smith, Martyn T ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Biomarkers; Chemical exposure; Risk assessment; Systems biology; Toxicogenomics

Indexed keywords

ARSENIC; BENZENE; BIOLOGICAL MARKER;

ENVIRONMENTAL EXPOSURE; GENOTYPE ENVIRONMENT INTERACTION; HAZARD ASSESSMENT; HEALTH HAZARD; PRIORITY JOURNAL; PROTEOMICS; REVIEW; RISK ASSESSMENT; TOXICOGENETICS; TRANSCRIPTOMICS;

ANIMALS; ARSENIC; BENZENE; ENVIRONMENTAL EXPOSURE; EPIGENESIS, GENETIC; FEMALE; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; MALE; PROTEOMICS; RISK ASSESSMENT; SYSTEMS BIOLOGY; TOXICOGENETICS; TOXICOLOGY;

ANIMALIA;

EID: 78650231595     PISSN: 13835742     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mrrev.2010.04.001     Document Type: Review

References (175)

1. Wild C.P. Complementing the genome with an "exposome": the outstanding challenge of environmental exposure measurement in molecular epidemiology. Cancer Epidemiol. Biomarkers Prev. 2005, 14:1847-1850.
2. Wray N.R., Goddard M.E., Visscher P.M. Prediction of individual genetic risk of complex disease. Curr. Opin. Genet. Dev. 2008, 18:257-263.
3. McCarroll S.A. Extending genome-wide association studies to copy-number variation. Hum. Mol. Genet. 2008, 17:R135-R142.
4. Tucker T., Marra M., Friedman J.M. Massively parallel sequencing: the next big thing in genetic medicine. Am. J. Hum. Genet. 2009, 85:142-154.
5. Robertson T.L., Kato H., Gordon T., Kagan A., Rhoads G.G., Land C.E., Worth R.M., Belsky J.L., Dock D.S., Miyanishi M., Kawamoto S. Epidemiologic studies of coronary heart disease and stroke in Japanese men living in Japan, Hawaii and California. Coronary heart disease risk factors in Japan and Hawaii. Am. J. Cardiol. 1977, 39:244-249.
6. Woo K.S., Chook P., Raitakari O.T., McQuillan B., Feng J.Z., Celermajer D.S. Westernization of Chinese adults and increased subclinical atherosclerosis. Arterioscler. Thromb. Vasc. Biol. 1999, 19:2487-2493.
7. Swerdlow A.J., Cooke K.R., Skegg D.C., Wilkinson J. Cancer incidence in England and Wales and New Zealand and in migrants between the two countries. Br. J. Cancer 1995, 72:236-243.
8. Gibson G. The environmental contribution to gene expression profiles. Nat. Rev. Genet. 2008, 9:575-581.
9. Hemminki K., Lorenzo Bermejo J., Forsti A. The balance between heritable and environmental aetiology of human disease. Nat. Rev. Genet. 2006, 7:958-965.
10. Smith M.T., Rappaport S.M. Building Exposure Biology Centers to Put the E into "G x E" Interaction Studies. Environ. Health Perspect. 2009, 117:A334-A335.
11. Hubal E.A. Biologically relevant exposure science for 21st century toxicity testing. Toxicol. Sci. 2009, 111:226-232.
12. Sheldon L.S., Cohen Hubal E.A. Exposure as part of a systems approach for assessing risk. Environ. Health Perspect. 2009, 117:119-1194.
13. Wild C.P. Environmental exposure measurement in cancer epidemiology. Mutagenesis 2009, 24:117-125.
14. Rubino F.M., Pitton M., Di Fabio D., Colombi A. Toward an "omic" physiopathology of reactive chemicals: Thirty years of mass spectrometric study of the protein adducts with endogenous and xenobiotic compounds. Mass Spectrom. Rev. 2009, 28:725-784.
15. Andreescu S., Njagi J., Ispas C., Ravalli M.T., Spotlight J.E.M. Applications of advanced nanomaterials for environmental monitoring. J. Environ. Monit. 2009, 11:27-40.
16. Mulvihill M., Tao A., Benjauthrit K., Arnold J., Yang P. Surface-enhanced Raman spectroscopy for trace arsenic detection in contaminated water. Angew. Chem. Int. Ed. Engl. 2008, 47:6456-6460.
17. Stockton A.M., Chiesl T.N., Scherer J.R., Mathies R.A. Polycyclic aromatic hydrocarbon analysis with the Mars organic analyzer microchip capillary electrophoresis system. Anal. Chem. 2009, 81:790-796.
18. Barry R.C., Lin Y., Wang J., Liu G., Timchalk C.A. Nanotechnology-based electrochemical sensors for biomonitoring chemical exposures. J. Exp. Sci. Environ. Epidemiol. 2009, 19:1-18.
19. GAO, EPA's Chemical Testing Program Has Made Little Progress, 1990, GA 1.13:RCED-90-112.
20. NRC, National Research Council Toxicity Testing: Strategies to Determine Needs and Priorities, National Academy Press, Washington, DC, 1984, pp. 382.
21. GAO, Chemical Regulation: Options Exist to Improve EPA's Ability to Assess Health Risks and Manage Its Chemical Review Program, 2005, GAO-05-458.
22. NRC, Scientific Frontiers in Developmental Toxicology and Risk Assessment, National Academy Press, Washington, DC, 2000, pp. 12.
23. Bhattacharya S., Coghlan A. One drug, six men, disaster. New Sci. 2006, 189:10-11.
24. FDA, Innovation or Stagnation: Challenge and Opportunity on the Critical Path to New Medical Products, 2004. http://www.fda.gov/oc/initiatives/criticalpath/whitepaper.html.
25. Katoh M., Tateno C., Yoshizato K., Yokoi T. Chimeric mice with humanized liver. Toxicology 2008, 246:9-17.
26. NRC, Toxicity Testing in the 21st Century" A vision and a Strategy, National Academy Press, Washington, DC, 2007.
27. NRC, Application of Toxicogenomic Technologies to Predictive Toxicology and Risk assessment, National Academy Press, Washington, DC, 2007.
28. EC, Regulation (EC) No 1907/2006 of the European Parliament and of the Council of 18 December 2006 concerning the Registration, Evaluation, Authorization, and Restriction of Chemicals (REACH), establishing a European Chemicals Agency, in: The European Parliament and the Council of the European Union, Off. J. Eur. Union, 2006.
29. Hartung T. A toxicology for the 21st century-mapping the road ahead. Toxicol. Sci. 2009, 109:18-23.
30. U.S. EPA, The U.S. Environmental Protection Agency's Strategic Plan for Evaluating the Toxicity of Chemicals, 2009. http://www.epa.gov/spc/toxicitytesting/.
31. NRC, Toxicity Testing for Assessment of Environmental Agents, National Academy Press, Washington, DC, 2006.
32. Clarke C.J., Haselden J.N. Metabolic profiling as a tool for understanding mechanisms of toxicity. Toxicol. Pathol. 2008, 36:140-147.
33. Gieger C., Geistlinger L., Altmaier E., Hrabe de Angelis M., Kronenberg F., Meitinger T., Mewes H.W., Wichmann H.E., Weinberger K.M., Adamski J., Illig T., Suhre K. Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum. PLoS Genet. 2008, 4:e1000282.
34. Holmes E., Loo R.L., Stamler J., Bictash M., Yap I.K., Chan Q., Ebbels T., De Iorio M., Brown I.J., Veselkov K.A., Daviglus M.L., Kesteloot H., Ueshima H., Zhao L., Nicholson J.K., Elliott P. Human metabolic phenotype diversity and its association with diet and blood pressure. Nature 2008, 453:396-400.
35. Wang-Sattler R., Yu Y., Mittelstrass K., Lattka E., Altmaier E., Gieger C., Ladwig K.H., Dahmen N., Weinberger K.M., Hao P., Liu L., Li Y., Wichmann H.E., Adamski J., Suhre K., Illig T. Metabolic profiling reveals distinct variations linked to nicotine consumption in humans-first results from the KORA study. PLoS ONE 2008, 3:e3863.
36. Blencowe B.J., Ahmad S., Lee L.J. Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes. Genes Dev. 2009, 23:1379-1386.
37. Shi L., Reid L.H., Jones W.D., Shippy R., Warrington J.A., Baker S.C., Collins P.J., de Longueville F., Kawasaki E.S., Lee K.Y., Luo Y., Sun Y.A., Willey J.C., Setterquist R.A., Fischer G.M., Tong W., Dragan Y.P., Dix D.J., Frueh F.W., Goodsaid F.M., Herman D., Jensen R.V., Johnson C.D., Lobenhofer E.K., Puri R.K., Schrf U., Thierry-Mieg J., Wang C., Wilson M., Wolber P.K., Zhang L., Amur S., Bao W., Barbacioru C.C., Lucas A.B., Bertholet V., Boysen C., Bromley B., Brown D., Brunner A., Canales R., Cao X.M., Cebula T.A., Chen J.J., Cheng J., Chu T.M., Chudin E., Corson J., Corton J.C., Croner L.J., Davies C., Davison T.S., Delenstarr G., Deng X., Dorris D., Eklund A.C., Fan X.H., Fang H., Fulmer-Smentek S., Fuscoe J.C., Gallagher K., Ge W., Guo L., Guo X., Hager J., Haje P.K., Han J., Han T., Harbottle H.C., Harris S.C., Hatchwell E., Hauser C.A., Hester S., Hong H., Hurban P., Jackson S.A., Ji H., Knight C.R., Kuo W.P., LeClerc J.E., Levy S., Li Q.Z., Liu C., Liu Y., Lombardi M.J., Ma Y., Magnuson S.R., Maqsodi B., McDaniel T., Mei N., Myklebost O., Ning B., Novoradovskaya N., Orr M.S., Osborn T.W., Papallo A., Patterson T.A., Perkins R.G., Peters E.H., Peterson R., Philips K.L., Pine P.S., Pusztai L., Qian F., Ren H., Rosen M., Rosenzweig B.A., Samaha R.R., Schena M., Schroth G.P., Shchegrova S., Smith D.D., Staedtler F., Su Z., Sun H., Szallasi Z., Tezak Z., Thierry-Mieg D., Thompson K.L., Tikhonova I., Turpaz Y., Vallanat B., Van C., Walker S.J., Wang S.J., Wang Y., Wolfinger R., Wong A., Wu J., Xiao C., Xie Q., Xu J., Yang W., Zhang L., Zhong S., Zong Y., Slikker W. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat. Biotechnol. 2006, 24:1151-1161.
38. Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball C.A., Causton H.C., Gaasterland T., Glenisson P., Holstege F.C., Kim I.F., Markowitz V., Matese J.C., Parkinson H., Robinson A., Sarkans U., Schulze-Kremer S., Stewart J., Taylor R., Vilo J., Vingron M. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet. 2001, 29:365-371.
39. Kawai T., Morita K., Masuda K., Nishida K., Shikishima M., Ohta M., Saito T., Rokutan K. Gene expression signature in peripheral blood cells from medical students exposed to chronic psychological stress. Biol Psychol 2007, 76:147-155.
40. Connolly P.H., Caiozzo V.J., Zaldivar F., Nemet D., Larson J., Hung S.P., Heck J.D., Hatfield G.W., Cooper D.M. Effects of exercise on gene expression in human peripheral blood mononuclear cells. J. Appl. Physiol. 2004, 97:1461-1469.
41. Zieker D., Fehrenbach E., Dietzsch J., Fliegner J., Waidmann M., Nieselt K., Gebicke-Haerter P., Spanagel R., Simon P., Niess A.M., Northoff H. cDNA microarray analysis reveals novel candidate genes expressed in human peripheral blood following exhaustive exercise. Physiol. Genom. 2005, 23:287-294.
42. Pagmantidis V., Meplan C., van Schothorst E.M., Keijer J., Hesketh J.E. Supplementation of healthy volunteers with nutritionally relevant amounts of selenium increases the expression of lymphocyte protein biosynthesis genes. Am J Clin Nutr 2008, 87:181-189.
43. Idaghdour Y., Storey J.D., Jadallah S.J., Gibson G. A genome-wide gene expression signature of environmental geography in leukocytes of Moroccan Amazighs. PLoS Genet. 2008, 4:e1000052.
44. Eady J.J., Wortley G.M., Wormstone Y.M., Hughes J.C., Astley S.B., Foxall R.J., Doleman J.F., Elliott R.M. Variation in gene expression profiles of peripheral blood mononuclear cells from healthy volunteers. Physiol. Genom. 2005, 22:402-411.
45. Forrest M.S., Lan Q., Hubbard A.E., Zhang L., Vermeulen R., Zhao X., Li G., Wu Y.Y., Shen M., Yin S., Chanock S.J., Rothman N., Smith M.T. Discovery of novel biomarkers by microarray analysis of peripheral blood mononuclear cell gene expression in benzene-exposed workers. Environ. Health Perspect. 2005, 113:801-807.
46. McHale C.M., Zhang L., Lan Q., Li G., Hubbard A.E., Forrest M.S., Vermeulen R., Chen J., Shen M., Rappaport S.M., Yin S., Smith M.T., Rothman N. Changes in the peripheral blood transcriptome associated with occupational benzene exposure identified by cross-comparison on two microarray platforms. Genomics 2009, 93:343-349.
47. McHale C.M., Zhang L., Hubbard A.E., Zhao X., Baccarelli A., Pesatori A.C., Smith M.T., Landi M.T. Microarray analysis of gene expression in peripheral blood mononuclear cells from dioxin-exposed human subjects. Toxicology 2007, 229:101-113.
48. Argos M., Kibriya M.G., Parvez F., Jasmine F., Rakibuz-Zaman M., Ahsan H. Gene expression profiles in peripheral lymphocytes by arsenic exposure and skin lesion status in a Bangladeshi population. Cancer Epidemiol. Biomarkers Prev. 2006, 15:1367-1375.
49. Lu T., Liu J., LeCluyse E.L., Zhou Y.S., Cheng M.L., Waalkes M.P. Application of cDNA microarray to the study of arsenic-induced liver diseases in the population of Guizhou, China. Toxicol. Sci. 2001, 59:185-192.
50. Wu M.M., Chiou H.Y., Ho I.C., Chen C.J., Lee T.C. Gene expression of inflammatory molecules in circulating lymphocytes from arsenic-exposed human subjects. Environ. Health Perspect. 2003, 111:1429-1438.
51. Wang Z., Neuburg D., Li C., Su L., Kim J.Y., Chen J.C., Christiani D.C. Global gene expression profiling in whole-blood samples from individuals exposed to metal fumes. Environ. Health Perspect. 2005, 113:233-241.
52. Lampe J.W., Stepaniants S.B., Mao M., Radich J.P., Dai H., Linsley P.S., Friend S.H., Potter J.D. Signatures of environmental exposures using peripheral leukocyte gene expression: tobacco smoke. Cancer Epidemiol. Biomarkers Prev. 2004, 13:445-453.
53. van Leeuwen D.M., van Agen E., Gottschalk R.W., Vlietinck R., Gielen M., van Herwijnen M.H., Maas L.M., Kleinjans J.C., van Delft J.H. Cigarette smoke-induced differential gene expression in blood cells from monozygotic twin pairs. Carcinogenesis 2007, 28:691-697.
54. Beane J., Sebastiani P., Liu G., Brody J.S., Lenburg M.E., Spira A. Reversible and permanent effects of tobacco smoke exposure on airway epithelial gene expression. Genome Biol. 2007, 8:R201.
55. Steiling K., Kadar A.Y., Bergerat A., Flanigon J., Sridhar S., Shah V., Ahmad Q.R., Brody J.S., Lenburg M.E., Steffen M., Spira A. Comparison of proteomic and transcriptomic profiles in the bronchial airway epithelium of current and never smokers. PLoS One 2009, 4:e5043.
56. Peretz A., Peck E.C., Bammler T.K., Beyer R.P., Sullivan J.H., Trenga C.A., Srinouanprachnah S., Farin F.M., Kaufman J.D. Diesel exhaust inhalation and assessment of peripheral blood mononuclear cell gene transcription effects: an exploratory study of healthy human volunteers. Inhal. Toxicol. 2007, 19:1107-1119.
57. van Leeuwen D.M., van Herwijnen M.H., Pedersen M., Knudsen L.E., Kirsch-Volders M., Sram R.J., Staal Y.C., Bajak E., van Delft J.H., Kleinjans J.C. Genome-wide differential gene expression in children exposed to air pollution in the Czech Republic. Mutat. Res. 2006, 600:12-22.
58. van Leeuwen D.M., Pedersen M., Hendriksen P.J., Boorsma A., van Herwijnen M.H., Gottschalk R.W., Kirsch-Volders M., Knudsen L.E., Sram R.J., Bajak E., van Delft J.H., Kleinjans J.C. Genomic analysis suggests higher susceptibility of children to air pollution. Carcinogenesis 2008, 29:977-983.
59. van Leeuwen D.M., Gottschalk R.W., van Herwijnen M.H., Moonen E.J., Kleinjans J.C., van Delft J.H. Differential gene expression in human peripheral blood mononuclear cells induced by cigarette smoke and its constituents. Toxicol. Sci. 2005, 86:200-210.
60. Hayes R.B., Songnian Y., Dosemeci M., Linet M. Benzene and lymphohematopoietic malignancies in humans. Am. J. Ind. Med. 2001, 40:117-126.
61. Glass D.C., Gray C.N., Jolley D.J., Gibbons C., Sim M.R., Fritschi L., Adams G.G., Bisby J.A., Manuell R. Leukemia risk associated with low-level benzene exposure. Epidemiology 2003, 14:569-577.
62. Savitz D.A., Andrews K.W. Review of epidemiologic evidence on benzene and lymphatic and hematopoietic cancers. Am. J. Ind. Med. 1997, 31:287-295.
63. Smith M.T., Jones R.M., Smith A.H. Benzene exposure and risk of non-Hodgkin lymphoma. Cancer Epidemiol. Biomarkers Prev. 2007, 16:385-391.
64. Lan Q., Zhang L., Li G., Vermeulen R., Weinberg R.S., Dosemeci M., Rappaport S.M., Shen M., Alter B.P., Wu Y., Kopp W., Waidyanatha S., Rabkin C., Guo W., Chanock S., Hayes R.B., Linet M., Kim S., Yin S., Rothman N., Smith M.T. Hematotoxicity in workers exposed to low levels of benzene. Science 2004, 306:1774-1776.
65. Zhang L., McHale C.M., Rothman N., Li G., Ji Z., Vermeulen R., Hubbard A.E., Ren X., Shen M., Rappaport S.M., North M., Skibola C.F., Yin S., Vulpe C., Chanock S.J., Smith M.T., Lan Q. Systems biology of human benzene exposure. Chemico-Biol. Interact. 2010, 184:86-93.
66. McHale C., Zhang L., Lan Q., Li G., Hubbard A., Porter K., Vermeulen R., Shen M., Rappaport S., Yin S., Smith M.T., Rothman N. Low-dose, occupational exposure to the leukemogen benzene induces robust changes in the blood transcriptome associated with altered immune system biology. Blood 2008, 112:1207.
67. Yoon B.I., Li G.X., Kitada K., Kawasaki Y., Igarashi K., Kodama Y., Inoue T., Kobayashi K., Kanno J., Kim D.Y., Inoue T., Hirabayashi Y. Mechanisms of benzene-induced hematotoxicity and leukemogenicity: cDNA microarray analyses using mouse bone marrow tissue. Environ. Health Perspect. 2003, 111:1411-1420.
68. Faiola B., Fuller E.S., Wong V.A., Recio L. Gene expression profile in bone marrow and hematopoietic stem cells in mice exposed to inhaled benzene. Mutat. Res. 2004, 549:195-212.
69. IARC, Overall evaluations of carcinogenicity: an updating of IARC Monographs volumes 1-42, IARC monographs on the evaluation of carcinogenic risks to humans 7 (1987) 1-440.
70. IARC, Some drinking-water disinfectants and contaminants, including arsenic, IARC Monogr. Eval. Carcinog. Risks Hum., 2004, pp. 1-477.
71. Pershagen G. The carcinogenicity of arsenic. Environ. Health Perspect. 1981, 40:93-100.
72. Smith A.H., Hopenhayn-Rich C., Bates M.N., Goeden H.M., Hertz-Picciotto I., Duggan H.M., Wood R., Kosnett M.J., Smith M.T. Cancer risks from arsenic in drinking water. Environ. Health Perspect. 1992, 97:259-267.
73. Ghosh P., Banerjee M., Giri A.K., Ray K. Toxicogenomics of arsenic: classical ideas and recent advances. Mutat. Res. 2008, 659:293-301.
74. NRC, Arsenic in drinking water 2001 update, National Academy Press, Washington, DC, 2001.
75. Andrew A.S., Jewell D.A., Mason R.A., Whitfield M.L., Moore J.H., Karagas M.R. Drinking-water arsenic exposure modulates gene expression in human lymphocytes from a U.S. population. Environ. Health Perspect. 2008, 116:524-531.
76. Chen C.J., Wang S.L., Chiou J.M., Tseng C.H., Chiou H.Y., Hsueh Y.M., Chen S.Y., Wu M.M., Lai M.S. Arsenic and diabetes and hypertension in human populations: a review. Toxicol. Appl. Pharmacol. 2007, 222:298-304.
77. Meliker J.R., Wahl R.L., Cameron L.L., Nriagu J.O. Arsenic in drinking water and cerebrovascular disease, diabetes mellitus, and kidney disease in Michigan: a standardized mortality ratio analysis. Environ. Health 2007, 6:4.
78. Hopenhayn C., Bush H.M., Bingcang A., Hertz-Picciotto I. Association between arsenic exposure from drinking water and anemia during pregnancy. J. Occup. Environ. Med. 2006, 48:635-643.
79. Rahman A., Vahter M., Ekstrom E.C., Rahman M., Golam Mustafa A.H., Wahed M.A., Yunus M., Persson L.A. Association of arsenic exposure during pregnancy with fetal loss and infant death: a cohort study in Bangladesh. Am. J. Epidemiol. 2007, 165:1389-1396.
80. Wasserman G.A., Liu X., Parvez F., Ahsan H., Factor-Litvak P., van Geen A., Slavkovich V., LoIacono N.J., Cheng Z., Hussain I., Momotaj H., Graziano J.H. Water arsenic exposure and children's intellectual function in Araihazar, Bangladesh. Environ. Health Perspect. 2004, 112:1329-1333.
81. Smith A.H., Marshall G., Yuan Y., Ferreccio C., Liaw J., von Ehrenstein O., Steinmaus C., Bates M.N., Selvin S. Increased mortality from lung cancer and bronchiectasis in young adults after exposure to arsenic in utero and in early childhood. Environ. Health Perspect. 2006, 114:1293-1296.
82. Liaw J., Marshall G., Yuan Y., Ferreccio C., Steinmaus C., Smith A.H. Increased childhood liver cancer mortality and arsenic in drinking water in northern Chile. Cancer Epidemiol. Biomarkers Prev. 2008, 17:1982-1987.
83. Bates M.N., Rey O.A., Biggs M.L., Hopenhayn C., Moore L.E., Kalman D., Steinmaus C., Smith A.H. Case-control study of bladder cancer and exposure to arsenic in Argentina. Am. J. Epidemiol. 2004, 159:381-389.
84. Vahter M. Health effects of early life exposure to arsenic. Basic Clin. Pharmacol. Toxicol. 2008, 102:204-211.
85. Fry R.C., Navasumrit P., Valiathan C., Svensson J.P., Hogan B.J., Luo M., Bhattacharya S., Kandjanapa K., Soontararuks S., Nookabkaew S., Mahidol C., Ruchirawat M., Samson L.D. Activation of inflammation/NF-kappaB signaling in infants born to arsenic-exposed mothers. PLoS Genet. 2007, 3:e207.
86. Gstaiger M., Aebersold R. Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat. Rev. Genet. 2009, 10:617-627.
87. Wingren C., Borrebaeck C.A. Antibody-based microarrays. Methods Mol. Biol. 2009, 509:57-84.
88. Merrick B.A. The plasma proteome, adductome and idiosyncratic toxicity in toxicoproteomics research. Brief Funct. Genomic Proteomic 2008, 7:35-49.
89. Issaq H.J., Xiao Z., Veenstra T.D. Serum and plasma proteomics. Chem. Rev. 2007, 107:3601-3620.
90. Ahmad S., Sundaramoorthy E., Arora R., Sen S., Karthikeyan G., Sengupta S. Progressive degradation of serum samples limits proteomic biomarker discovery. Anal. Biochem. 2009, 394:237-242.
91. Taylor C.F., Paton N.W., Lilley K.S., Binz P.A., Julian R.K., Jones A.R., Zhu W., Apweiler R., Aebersold R., Deutsch E.W., Dunn M.J., Heck A.J., Leitner A., Macht M., Mann M., Martens L., Neubert T.A., Patterson S.D., Ping P., Seymour S.L., Souda P., Tsugita A., Vandekerckhove J., Vondriska T.M., Whitelegge J.P., Wilkins M.R., Xenarios I., Yates J.R., Hermjakob H. The minimum information about a proteomics experiment (MIAPE). Nat. Biotechnol. 2007, 25:887-893.
92. Orchard S., Binz P.A., Hermjakob H. Second Joint HUPO Publication and Proteomics Standards Initiative Workshop. Proteomics 2009, 9:4428-14428.
93. Vermeulen R., Lan Q., Zhang L., Gunn L., McCarthy D., Woodbury R.L., McGuire M., Podust V.N., Li G., Chatterjee N., Mu R., Yin S., Rothman N., Smith M.T. Decreased levels of CXC-chemokines in serum of benzene-exposed workers identified by array-based proteomics. Proc. Natl. Acad. Sci. U. S. A. 2005, 102:17041-17046.
94. Hegedus C.M., Skibola C.F., Warner M., Skibola D.R., Alexander D., Lim S., Dangleben N.L., Zhang L., Clark M., Pfeiffer R.M., Steinmaus C., Smith A.H., Smith M.T., Moore L.E. Decreased urinary beta-defensin-1 expression as a biomarker of response to arsenic. Toxicol. Sci. 2008, 106:74-82.
95. Harezlak J., Wu M.C., Wang M., Schwartzman A., Christiani D.C., Lin X. Biomarker discovery for arsenic exposure using functional data. Analysis and feature learning of mass spectrometry proteomic data. J. Proteome Res. 2008, 7:217-224.
96. Zhai R., Su S., Lu X., Liao R., Ge X., He M., Huang Y., Mai S., Lu X., Christiani D. Proteomic profiling in the sera of workers occupationally exposed to arsenic and lead: identification of potential biomarkers. Biometals 2005, 18:603-613.
97. Joo W.A., Sul D., Lee D.Y., Lee E., Kim C.W. Proteomic analysis of plasma proteins of workers exposed to benzene. Mutat. Res. 2004, 558:35-44.
98. Fleischer J., Grage-Griebenow E., Kasper B., Heine H., Ernst M., Brandt E., Flad H.D., Petersen F. Platelet factor 4 inhibits proliferation and cytokine release of activated human T cells. J. Immunol. 2002, 169:770-777.
99. Ehlert J.E., Ludwig A., Grimm T.A., Lindner B., Flad H.D., Brandt E. Down-regulation of neutrophil functions by the ELR(+) CXC chemokine platelet basic protein. Blood 2000, 96:2965-2972.
100. Han Z.C., Lu M., Li J., Defard M., Boval B., Schlegel N., Caen J.P. Platelet factor 4 and other CXC chemokines support the survival of normal hematopoietic cells and reduce the chemosensitivity of cells to cytotoxic agents. Blood 1997, 89:2328-2335.
101. Valore E.V., Park C.H., Quayle A.J., Wiles K.R., McCray P.B., Ganz T. Human beta-defensin-1: an antimicrobial peptide of urogenital tissues. J. Clin. Invest. 1998, 101:1633-1642.
102. Yang D., Chertov O., Bykovskaia S.N., Chen Q., Buffo M.J., Shogan J., Anderson M., Schroder J.M., Wang J.M., Howard O.M., Oppenheim J.J. Beta-defensins: linking innate and adaptive immunity through dendritic and T cell CCR6. Science 1999, 286:525-528.
103. Zucht H.D., Grabowsky J., Schrader M., Liepke C., Jurgens M., Schulz-Knappe P., Forssmann W.G. Human beta-defensin-1: A urinary peptide present in variant molecular forms and its putative functional implication. Eur. J. Med. Res. 1998, 3:315-323.
104. Kim K.C., Friso S., Choi S.W. DNA methylation, an epigenetic mechanism connecting folate to healthy embryonic development and aging. J. Nutr. Biochem. 2009, 20:917-926.
105. Davis C.D., Uthus E.O. DNA methylation, cancer susceptibility, and nutrient interactions. Exp. Biol. Med. (Maywood) 2004, 229:988-995.
106. Fraga M.F., Esteller M. Epigenetics and aging: the targets and the marks. Trends Genet. 2007, 23:413-418.
107. Fraga M.F., Ballestar E., Paz M.F., Ropero S., Setien F., Ballestar M.L., Heine-Suner D., Cigudosa J.C., Urioste M., Benitez J., Boix-Chornet M., Sanchez-Aguilera A., Ling C., Carlsson E., Poulsen P., Vaag A., Stephan Z., Spector T.D., Wu Y.Z., Plass C., Esteller M. Epigenetic differences arise during the lifetime of monozygotic twins. Proc. Natl. Acad. Sci. U. S. A. 2005, 102:10604-10609.
108. Jirtle R.L., Skinner M.K. Environmental epigenomics and disease susceptibility. Nat. Rev. Genet. 2007, 8:253-262.
109. Szyf M. The dynamic epigenome and its implications in toxicology. Toxicol. Sci. 2007, 100:7-23.
110. Sridhar S., Schembri F., Zeskind J., Shah V., Gustafson A.M., Steiling K., Liu G., Dumas Y.M., Zhang X., Brody J.S., Lenburg M.E., Spira A. Smoking-induced gene expression changes in the bronchial airway are reflected in nasal and buccal epithelium. BMC Genom. 2008, 9:259.
111. Schembri F., Sridhar S., Perdomo C., Gustafson A.M., Zhang X., Ergun A., Lu J., Liu G., Zhang X., Bowers J., Vaziri C., Ott K., Sensinger K., Collins J.J., Brody J.S., Getts R., Lenburg M.E., Spira A. MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:2319-2324.
112. Beck S., Rakyan V.K. The methylome: approaches for global DNA methylation profiling. Trends Genet. 2008, 24:231-237.
113. Kong W., Zhao J.J., He L., Cheng J.Q. Strategies for profiling microRNA expression. J. Cell Physiol. 2009, 218:22-25.
114. Galm O., Herman J.G., Baylin S.B. The fundamental role of epigenetics in hematopoietic malignancies. Blood Rev. 2006, 20:1-13.
115. Mulero-Navarro S., Esteller M. Epigenetic biomarkers for human cancer: the time is now. Crit. Rev. Oncol. Hematol. 2008, 68:1-11.
116. Vaissiere T., Hung R.J., Zaridze D., Moukeria A., Cuenin C., Fasolo V., Ferro G., Paliwal A., Hainaut P., Brennan P., Tost J., Boffetta P., Herceg Z. Quantitative analysis of DNA methylation profiles in lung cancer identifies aberrant DNA methylation of specific genes and its association with gender and cancer risk factors. Cancer Res. 2009, 69:243-252.
117. Edwards T.M., Myers J.P. Environmental exposures and gene regulation in disease etiology. Environ. Health Perspect. 2007, 115:1264-1270.
118. Brait M., Ford J.G., Papaiahgari S., Garza M.A., Lee J.I., Loyo M., Maldonado L., Begum S., McCaffrey L., Howerton M., Sidransky D., Emerson M.R., Ahmed S., Williams C.D., Hoque M.O. Association between lifestyle factors and CpG island methylation in a cancer-free population. Cancer Epidemiol. Biomarkers Prev. 2009, 18:2984-2991.
119. Lu J., Getz G., Miska E.A., Alvarez-Saavedra E., Lamb J., Peck D., Sweet-Cordero A., Ebert B.L., Mak R.H., Ferrando A.A., Downing J.R., Jacks T., Horvitz H.R., Golub T.R. MicroRNA expression profiles classify human cancers. Nature 2005, 435:834-838.
120. Volinia S., Calin G.A., Liu C.G., Ambs S., Cimmino A., Petrocca F., Visone R., Iorio M., Roldo C., Ferracin M., Prueitt R.L., Yanaihara N., Lanza G., Scarpa A., Vecchione A., Negrini M., Harris C.C., Croce C.M. A microRNA expression signature of human solid tumors defines cancer gene targets. Proc. Natl. Acad. Sci. U. S. A. 2006, 103:2257-2261.
121. Calin G.A., Ferracin M., Cimmino A., Di Leva G., Shimizu M., Wojcik S.E., Iorio M.V., Visone R., Sever N.I., Fabbri M., Iuliano R., Palumbo T., Pichiorri F., Roldo C., Garzon R., Sevignani C., Rassenti L., Alder H., Volinia S., Liu C.G., Kipps T.J., Negrini M., Croce C.M. A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N. Engl. J. Med. 2005, 353:1793-1801.
122. Garzon R., Croce C.M. MicroRNAs in normal and malignant hematopoiesis. Curr. Opin. Hematol. 2008, 15:352-358.
123. Tili E., Michaille J.J., Costinean S., Croce C.M. MicroRNAs, the immune system and rheumatic disease. Nat. Clin. Pract. Rheumatol. 2008, 4:534-541.
124. Erson A.E., Petty E.M. MicroRNAs in development and disease. Clin. Genet. 2008, 74:296-306.
125. Bollati V., Baccarelli A., Hou L., Bonzini M., Fustinoni S., Cavallo D., Byun H.M., Jiang J., Marinelli B., Pesatori A.C., Bertazzi P.A., Yang A.S. Changes in DNA methylation patterns in subjects exposed to low-dose benzene. Cancer Res. 2007, 67:876-880.
126. Muller C.I., Luong Q.T., Shih L.Y., Jones L.C., Desmond J.C., Kawamata N., Tcherniantchouk O., Liu Q., Ito K., Osato M., Ito Y., Tefferi A., de Vos S., Koeffler H.P. Identification of marker genes including RUNX3 (AML2) that discriminate between different myeloproliferative neoplasms and normal individuals. Leukemia 2008, 22:1773-1778.
127. Neufeld G., Shraga-Heled N., Lange T., Guttmann-Raviv N., Herzog Y., Kessler O. Semaphorins in cancer. Front. Biosci. 2005, 10:751-760.
128. Chanda S., Dasgupta U.B., Guhamazumder D., Gupta M., Chaudhuri U., Lahiri S., Das S., Ghosh N., Chatterjee D. DNA hypermethylation of promoter of gene p53 and p16 in arsenic-exposed people with and without malignancy. Toxicol. Sci. 2006, 89:431-437.
129. Chai C.Y., Huang Y.C., Hung W.C., Kang W.Y., Chen W.T. Arsenic salts induced autophagic cell death and hypermethylation of DAPK promoter in SV-40 immortalized human uroepithelial cells. Toxicol. Lett. 2007, 173:48-56.
130. Chen W.T., Hung W.C., Kang W.Y., Huang Y.C., Chai C.Y. Urothelial carcinomas arising in arsenic-contaminated areas are associated with hypermethylation of the gene promoter of the death-associated protein kinase. Histopathology 2007, 51:785-792.
131. Marsit C.J., Karagas M.R., Schned A., Kelsey K.T. Carcinogen exposure and epigenetic silencing in bladder cancer. Ann. N. Y. Acad. Sci. 2006, 1076:810-821.
132. Kile M.L., Ronnenberg A.G. Can folate intake reduce arsenic toxicity?. Nutr. Rev. 2008, 66:349-353.
133. Marsit C.J., Eddy K., Kelsey K.T. MicroRNA responses to cellular stress. Cancer Res. 2006, 66:10843-10848.
134. NRC, Science and decisions: Advancing risk assessment, 2008.
135. Weisburger E.K. History of the Bioassay Program of the National Cancer Institute. Prog. Exp. Tumor Res. 1983, 26:187-201.
136. Muller L., Kikuchi Y., Probst G., Schechtman L., Shimada H., Sofuni T., Tweats D. ICH-harmonised guidances on genotoxicity testing of pharmaceuticals: evolution, reasoning and impact. Mutat. Res. 1999, 436:195-225.
137. Ellinger-Ziegelbauer H., Aubrecht J., Kleinjans J.C., Ahr H.J. Application of toxicogenomics to study mechanisms of genotoxicity and carcinogenicity. Toxicol. Lett. 2009, 186:36-44.
138. Fielden M.R., Nie A., McMillian M., Elangbam C.S., Trela B.A., Yang Y., Dunn R.T., Dragan Y., Fransson-Stehen R., Bogdanffy M., Adams S.P., Foster W.R., Chen S.J., Rossi P., Kasper P., Jacobson-Kram D., Tatsuoka K.S., Wier P.J., Gollub J., Halbert D.N., Roter A., Young J.K., Sina J.F., Marlowe J., Martus H.J., Aubrecht J., Olaharski A.J., Roome N., Nioi P., Pardo I., Snyder R., Perry R., Lord P., Mattes W., Car B.D. Interlaboratory evaluation of genomic signatures for predicting carcinogenicity in the rat. Toxicol. Sci. 2008, 103:28-34.
139. Fielden M.R., Brennan R., Gollub J. A gene expression biomarker provides early prediction and mechanistic assessment of hepatic tumor induction by nongenotoxic chemicals. Toxicol. Sci. 2007, 99:90-100.
140. Tsujimura K., Asamoto M., Suzuki S., Hokaiwado N., Ogawa K., Shirai T. Prediction of carcinogenic potential by a toxicogenomic approach using rat hepatoma cells. Cancer Sci. 2006, 97:1002-1010.
141. Nakayama K., Kawano Y., Kawakami Y., Moriwaki N., Sekijima M., Otsuka M., Yakabe Y., Miyaura H., Saito K., Sumida K., Shirai T. Differences in gene expression profiles in the liver between carcinogenic and non-carcinogenic isomers of compounds given to rats in a 28-day repeat-dose toxicity study. Toxicol. Appl. Pharmacol. 2006, 217:299-307.
142. Ellinger-Ziegelbauer H., Stuart B., Wahle B., Bomann W., Ahr H.J. Comparison of the expression profiles induced by genotoxic and nongenotoxic carcinogens in rat liver. Mutat. Res. 2005, 575:61-84.
143. Mattingly C.J., Rosenstein M.C., Colby G.T., Forrest J.N., Boyer J.L. The Comparative Toxicogenomics Database (CTD): a resource for comparative toxicological studies. J. Exp. Zool. A Comp. Exp. Biol. 2006, 305:689-692.
144. Waters M., Stasiewicz S., Merrick B.A., Tomer K., Bushel P., Paules R., Stegman N., Nehls G., Yost K.J., Johnson C.H., Gustafson S.F., Xirasagar S., Xiao N., Huang C.C., Boyer P., Chan D.D., Pan Q., Gong H., Taylor J., Choi D., Rashid A., Ahmed A., Howle R., Selkirk J., Tennant R., Fostel J. CEBS-Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data. Nucleic Acids Res. 2008, 36:D892-D900.
145. Crump K.S., Chiu W.A., Subramaniam R.P. Issues in using human variability distributions to estimate low-dose risk. Environmental Health Perspectives 2010, 118:387-393.
146. Funk W.E., Waidyanatha S., Chaing S.H., Rappaport S.M. Hemoglobin adducts of benzene oxide in neonatal and adult dried blood spots. Cancer Epidemiol. Biomarkers Prev. 2008, 17:1896-1901.
147. Lin Y.S., Vermeulen R., Tsai C.H., Waidyanatha S., Lan Q., Rothman N., Smith M.T., Zhang L., Shen M., Li G., Yin S., Kim S., Rappaport S.M.
148. Guyton K.Z., Kyle A.D., Aubrecht J., Cogliano V.J., Eastmond D.A., Jackson M., Keshava N., Sandy M.S., Sonawane B., Zhang L., Waters M.D., Smith M.T. Improving prediction of chemical carcinogenicity by considering multiple mechanisms and applying toxicogenomic approaches. Mutat. Res. 2009, 681:230-240.
149. Rappaport S.M., Kim S., Lan Q., Vermeulen R., Waidyanatha S., Zhang L., Li G., Yin S., Hayes R.B., Rothman N., Smith M.T. Evidence that humans metabolize benzene via two pathways. Environ. Health Perspect. 2009, 117:946-952.
150. Edwards S.W., Preston R.J. Systems biology and mode of action based risk assessment. Toxicol. Sci. 2008, 106:312-318.
151. Dudley J.T., Butte A.J. Identification of discriminating biomarkers for human disease using integrative network biology. Pac. Symp. Biocomput. 2009, 27-38.
152. Gohlke J.M., Thomas R., Zhang Y., Rosenstein M.C., Davis A.P., Murphy C., Becker K.G., Mattingly C.J., Portier C.J. Genetic and environmental pathways to complex diseases. BMC Syst. Biol. 2009, 3:46.
153. Sjoblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D., Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S., Buckhaults P., Farrell C., Meeh P., Markowitz S.D., Willis J., Dawson D., Willson J.K., Gazdar A.F., Hartigan J., Wu L., Liu C., Parmigiani G., Park B.H., Bachman K.E., Papadopoulos N., Vogelstein B., Kinzler K.W., Velculescu V.E. The consensus coding sequences of human breast and colorectal cancers. Science 2006, 314:268-274.
154. Jones S., Zhang X., Parsons D.W., Lin J.C., Leary R.J., Angenendt P., Mankoo P., Carter H., Kamiyama H., Jimeno A., Hong S.M., Fu B., Lin M.T., Calhoun E.S., Kamiyama M., Walter K., Nikolskaya T., Nikolsky Y., Hartigan J., Smith D.R., Hidalgo M., Leach S.D., Klein A.P., Jaffee E.M., Goggins M., Maitra A., Iacobuzio-Donahue C., Eshleman J.R., Kern S.E., Hruban R.H., Karchin R., Papadopoulos N., Parmigiani G., Vogelstein B., Velculescu V.E., Kinzler K.W. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 2008, 321:1801-1806.
155. Davidsson J., Lilljebjorn H., Andersson A., Veerla S., Heldrup J., Behrendtz M., Fioretos T., Johansson B. The DNA methylome of pediatric acute lymphoblastic leukemia. Hum. Mol. Genet. 2009, 18:4054-4065.
156. Mohr S., Liew C.C. The peripheral-blood transcriptome: new insights into disease and risk assessment. Trends Mol. Med. 2007, 13:422-432.
157. Pedersen-Bjergaard J., Andersen M.K., Andersen M.T., Christiansen D.H. Genetics of therapy-related myelodysplasia and acute myeloid leukemia. Leukemia 2008, 22:240-248.
158. Becker K.G., Barnes K.C., Bright T.J., Wang S.A. The genetic association database. Nat. Genet. 2004, 36:431-432.
159. Lund E., Dumeaux V. Systems epidemiology in cancer. Cancer Epidemiol. Biomarkers Prev. 2008, 17:2954-2957.
160. Ioannidis J.P. Why most published research findings are false. PLoS Med. 2005, 2:e124.
161. Kinross J.M., von Roon A.C., Holmes E., Darzi A., Nicholson J.K. The human gut microbiome: implications for future health care. Curr. Gastroenterol. Rep. 2008, 10:396-403.
162. Vineis P., Airoldi L., Veglia F., Olgiati L., Pastorelli R., Autrup H., Dunning A., Garte S., Gormally E., Hainaut P., Malaveille C., Matullo G., Peluso M., Overvad K., Tjonneland A., Clavel-Chapelon F., Boeing H., Krogh V., Palli D., Panico S., Tumino R., Bueno-De-Mesquita B., Peeters P., Berglund G., Hallmans G., Saracci R., Riboli E. Environmental tobacco smoke and risk of respiratory cancer and chronic obstructive pulmonary disease in former smokers and never smokers in the EPIC prospective study. BMJ 2005, 330:277.
163. Westfall P.H., Young S.S. Resampling-based Multiple Testing: Examples and Methods for p-value Adjustment 1993, John Wiley and Sons, Hoboken, NJ.
164. Benjamini Y., Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B. 1995, 57:289-300.
165. Chen J., van der Laan M.J., Smith M.T., Hubbard A.E. A comparison of methods to control type I errors in microarray studies. Stat. Appl. Genet. Mol. Biol. 2007, 6. (Article28).
166. van der Laan M.J., Hubbard A.E. Quantile-function based null distribution in resampling based multiple testing. Stat. Appl. Genet. Mol. Biol. 2006, 5. (Article14).
167. C. Tuglus, M.J. Van der Laan, Targeted Methods for Biomarker Discovery, the Search for a Standard, U.C. Berkeley Division of Biostatistics Working Paper Series, 2008. Working Paper 233.
168. Kaufman L., Rousseeuw P. Finding Groups in Data: An Introduction to Cluster Analys 1990, John Wiley and Sons, New York.
169. Subramanian A., Tamayo P., Mootha V.K., Mukherjee S., Ebert B.L., Gillette M.A., Paulovich A., Pomeroy S.L., Golub T.R., Lander E.S., Mesirov J.P. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. U. S. A. 2005, 102:15545-15550.
170. Mootha V.K., Lindgren C.M., Eriksson K.F., Subramanian A., Sihag S., Lehar J., Puigserver P., Carlsson E., Ridderstrale M., Laurila E., Houstis N., Daly M.J., Patterson N., Mesirov J.P., Golub T.R., Tamayo P., Spiegelman B., Lander E.S., Hirschhorn J.N., Altshuler D., Groop L.C. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet. 2003, 34:267-273.
171. Balasubramanian R., LaFramboise T., Scholtens D., Gentleman R. A graph-theoretic approach to testing associations between disparate sources of functional genomics data. Bioinformatics 2004, 20:3353-3362.
172. Zeeberg B.R., Feng W., Wang G., Wang M.D., Fojo A.T., Sunshine M., Narasimhan S., Kane D.W., Reinhold W.C., Lababidi S., Bussey K.J., Riss J., Barrett J.C., Weinstein J.N. GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol 2003, 4:R28.
173. NIH, NIH Roadmap for Medical Research: Epigenomics, 2007. http://nihroadmap.nih.gov/epigenomics/.
174. Rosser C.J., Liu L., Sun Y., Villicana P., McCullers M., Porvasnik S., Young P.R., Parker A.S., Goodison S. Bladder cancer-associated gene expression signatures identified by profiling of exfoliated urothelia. Cancer Epidemiol. Biomarkers Prev. 2009, 18:444-453.
175. Rim K.T., Park K.K., Kim Y.H., Lee Y.H., Han J.H., Chung Y.H., Yu I.J. Gene-expression profiling of human mononuclear cells from welders using cDNA microarray. J. Toxicol. Environ. Health A 2007, 70:1264-1277.